[gmx-users] Analysis of Protein Complex

[Tsjerk Wassenaar]

Hi Saba,

You can use g_mdmat or run g_rmsdist for different time windows.
It's also a good idea to have a look at all the analysis tools and
think of how they may suit your purpose.

Cheers,

Tsjerk

On Thu, Dec 1, 2011 at 5:43 AM, Saba Ferdous <saba.bsbi154 at iiu.edu.pk> wrote:
> Dear Sir,
> I am studying a protein complex. I have perforemed 10ns simulations. I saved
> snapshots every10ps. sp all snap shopts I got were 1000.
> Now I want to analyse them with respect to interactions. I want to check the
> binding surfaces and binding points which come closer and incontact during
> simulations. Can you devise me a way to perform such kind of analysis.
> Further more I am interested to know the binding energies as well. What sort
> of other analysis can be done on this complex.
>
> --
> Saba Ferdous
> Research Scholar (M. Phil)
> National Center for Bioinformatics
> Quaid-e-Azam University, Islamabad
> Pakistan
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands